Like most days, JJ very politely pointed out that I am a wrong this
morning. You can have variable numbers of outputs at runtime, see the
last section ("Number of Output datasets cannot be determined until
tool run"
) of this page:

http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files

Sorry about that.

-John

On Tue, Oct 16, 2012 at 8:48 AM, John Chilton <chil0...@umn.edu> wrote:
> I don't believe this is possible in Galaxy right now. Are the outputs
> independent or is information from all inputs used to produce all
> outputs? If they are independent, you can create a workflow containing
> just your tool with 1 input and 1 output and use the batch workflow
> mode to run it on multiple files and get multiple outputs. This is not
> a beautiful solution but it gets the job done in some cases.
>
> Another thing to look at might be the discussion we are having on the
> thread "pass more information on a dataset merge". We have a fork (its
> all work from Jorrit Boekel) of galaxy that creates composite
> datatypes for each explicitly defined type that can hold collections
> of a single type.
>
> https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes/compare
>
> This would hopefully let you declare that you can accept a collection
> of whatever your input type is and produce a collection of whatever
> your output is. Lots of downsides to this approach - not fully
> implemented, and not included in Galaxy proper, your outputs would be
> wrapped up in a composite datatype so they wouldn't be easily
> processable by downstream tools. It would be good to have additional
> people hacking on it though :)
>
> -John
>
> ------------------------------------------------
> John Chilton
> Senior Software Developer
> University of Minnesota Supercomputing Institute
> Office: 612-625-0917
> Cell: 612-226-9223
> Bitbucket: https://bitbucket.org/jmchilton
> Github: https://github.com/jmchilton
> Web: http://jmchilton.net
>
> On Tue, Oct 16, 2012 at 7:13 AM, Sascha Kastens
> <s.kast...@gatc-biotech.com> wrote:
>> Hi all!
>>
>>
>>
>> I have a tool which takes one ore more input files. For each input file one
>> output is created,
>>
>> i.e. 1 input file -> 1 output file, 2 input files -> 2 output files, etc.
>>
>>
>>
>> What is the best way to handle this? I used the directions for handlin
>> multiple output files where
>>
>> the ’Number of Output datasets cannot be determined until tool run’ which in
>> my opinion is a bit
>>
>> inappropriate. BTW: The input files are added via the <repeat>-Tag, so maybe
>> there is a similar
>>
>> thing for outputs?
>>
>>
>>
>> Thanks in advance!
>>
>>
>>
>> Cheers,
>>
>> Sascha
>>
>>
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